Yun entered politics in 1945 following Gwangbokjeol (Liberation Day). The first Doctor of Philosophy from Princeton University in Korea, as well as first President of South Korea, Dr. Syngman Rhee, was his mentor. By 1947, Yun was serving as Secretary to the Korean Chief of Staff. In 1948, Rhee appointed Yun to the position of mayor of Seoul. A year later, he was made Minister of Commerce and Industry. However, Yun soon began to disagree with Rhee's authoritarian policies.

While serving as president of the Red Cross Society, he was elected to the National Assembly in 1954. A year later, he co-founded the opposition South Korean Democratic Party. In 1959, he became a representative to the Supreme Council of the Democratic Party.

Rhee's government was ousted by a student-led, pro-democracy uprising in 1960; and Yun was elected president on August 13, and appointed Chang Myon as First Minister. In response to the authoritarian excesses of Rhee's regime, South Korea had switched to a parliamentary system; so in fact Yun served merely as a figurehead.

Following Park Chung Hee's coup in 1961, Yun stayed in his post in order to provide some legitimacy to the new regime, but resigned on March 22, 1962. In the following years, Yun received suspended sentences several times for anti-government activities. He opposed Park's authoritarian rule[1] and ran for president twice, in 1963 and 1967, losing each time.

Yun retired from active politics in 1980 and focused his life on cultural activities until his death on July 18, 1990.[2]